NM_001127898.4(CLCN5):c.1422G>A (p.Glu474=) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Oct 20, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002480258.1

Allele description [Variation Report for NM_001127898.4(CLCN5):c.1422G>A (p.Glu474=)]

NM_001127898.4(CLCN5):c.1422G>A (p.Glu474=)

Gene:

CLCN5:chloride voltage-gated channel 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.23

Genomic location:

Preferred name:

NM_001127898.4(CLCN5):c.1422G>A (p.Glu474=)

HGVS:

NC_000023.11:g.50086735G>A
NG_007159.3:g.169120G>A
NM_000084.5:c.1212G>A
NM_001127898.4:c.1422G>AMANE SELECT
NM_001127899.4:c.1422G>A
NM_001282163.2:c.1272G>A
NP_000075.1:p.Glu404=
NP_001121370.1:p.Glu474=
NP_001121371.1:p.Glu474=
NP_001269092.1:p.Glu424=
NC_000023.10:g.49851392G>A
NM_000084.2:c.1212G>A
NM_000084.3:c.1212G>A
NM_000084.4:c.1212G>A

Links:

dbSNP: rs199594074

NCBI 1000 Genomes Browser:

rs199594074

Molecular consequence:

NM_000084.5:c.1212G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127898.4:c.1422G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127899.4:c.1422G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001282163.2:c.1272G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Dent disease type 1
Synonyms:: NEPHROLITHIASIS, HYPERCALCIURIC, X-LINKED; Nephrolithiasis, hypercalciuria X-linked; Urolithiasis, hypercalciuric X-linked; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010225; MedGen: C1848336; Orphanet: 1652; Orphanet: 93622; OMIM: 300009

Name:: Hypophosphatemic rickets, X-linked recessive (XLHRR)
Synonyms:: Rickets, hypophosphataemic
Identifiers:: MONDO: MONDO:0010358; MedGen: C1845168; Orphanet: 1652; Orphanet: 93622; OMIM: 300554

Name:: X-linked recessive nephrolithiasis with renal failure (XRN)
Synonyms:: NEPHROLITHIASIS 1; NEPHROLITHIASIS, X-LINKED RECESSIVE, TYPE 1; UROLITHIASIS, X-LINKED RECESSIVE, TYPE 1
Identifiers:: MONDO: MONDO:0010687; MedGen: C0403720; Orphanet: 1652; Orphanet: 93622; OMIM: 310468

Name:: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
Identifiers:: MONDO: MONDO:0010644; MedGen: C1839874; Orphanet: 1652; Orphanet: 93622; OMIM: 308990

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002802808	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 20, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002802808

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Oct 20, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV002802808.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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